Chapter 2

CHEMISTRYCHEMISTRY

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WHY is there a CHEMISTRY

chapter in my Biology book?

• Structure and function of all living things are governed by the laws of chemistry

• QUESTION: What examples can you give of how chemistry is involved in biology?

• Understanding the basic principles of chemistry will give you a better understanding of all living things and how they function!

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CHEMISTRY- The science of the composition, structure, properties, and reactions of matter

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• Matter • is anything that has weight and

takes up space• Elements • are the basic building blocks of

matter that cannot be broken down by chemical means

• Atoms • are the smallest units of an

element that retain the element’s physical and chemical properties. • These bond together to form

molecules

ElementsElements• Pure substances than

cannot be broken down into simpler substances

• Periodic Table categorizes elements and shows trends

• Currently, there are 118

elements, 92 which occur naturally

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Biologists love CHONPS CHONPS most of all!

• 90% of the mass of living things are composed of combinations of 4 elements: O,C, H, & N

• Throw in P and S and you can make almost any combination of organic molecules!– Carbs– Lipids– Nucleic acids– Amino acids, proteins

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AtomsAtoms• Simplest part of an element that retains all

properties of that element• Too small to see so we make up models to help us

understand the structure of atoms and predict how they will act

• Subatomic particles:• Neutrons have a neutral charge• Protons are positively charged

• Neutrons and protons make up the nucleus• Electrons are negatively charged and orbit

around the nucleus

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Subatomic particles of atoms

Normally, #e = #p = #n

HOWEVER, some atoms of certain elements may have “extra” neutrons in their nucleus…

…this will slightly change their atomic _________; they are called ______________

2.1 From atoms to molecules

Isotopes• Isotopes are atoms that have

the same atomic number but a different atomic mass because the number of neutrons differ

• Examples: 14C/12C, 127I, 131I

• Radioactive isotopes are useful in dating old objects, sterilizing food, imaging body organs and tissues through x-rays and killing cancer cells

• Types of radiation can be harmful by damaging cells and DNA and/or causing cancer

2.1 From atoms to molecules

larynx

thyroid gland

trachea

b.

a.

a: © Biomed Commun./Custom Medical Stock Photo; b(patient): Courtesy National Institutes of Health (NIH); b(brain scan): © Mazzlota et al./Photo Researchers, Inc.

Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.

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Different elements are used in medical contrast

imaging

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IodineBarium

Molecules• Most elements do not exist by

themselves in nature but rather like to combine with other elements

• “Molecules” are made of atoms that are bonded together

• Can be made of the same atom or different atoms

2.1 From atoms to molecules

CompoundsCompounds• A molecule is formed when two or more atoms join together

chemically.• Example, oxygen gas, O2

• A compound is a molecule that contains at least two different elements. All compounds are molecules but not all molecules are compounds.• Ex: WATER. 2 H atoms + 1 O atom = 1 H2O molecule

• Chemical properties of compounds are often very different than the elements alone (2 gases = liquid)

• “Chemical reactions”- chemical bonds can be broken, atoms can be rearranged, and new chemical bonds are formed!

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Types of Chemical BondsTypes of Chemical Bonds• Most bonding takes place because atoms are most

chemically stable when their outermost energy levels are filled

• “Octet” rule• Ex: Fluorine (7 outer e-)

• Covalent bonds: – Strong bonds– Shared electrons, simulate a full outer orbital

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Ionic BondsIonic Bonds

• Create ions• Na becomes (Na+) = loses e-

• Cl becomes (Cl-)= gains an e-

• Create electrical charges: when + and – charges attract, ionic bonds are created

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States of MatterStates of Matter• SOLID: molecules are tightly linked; little movement and

definite shape• LIQUID: molecules are less tightly linked; moves more freely

than solids; conforms to container• GAS: molecules are usually not attracted to one another;

move very fast; fills the entire volume of a container

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WATERWATER • Living things are 70-80% water by weight• Most chemical rxns in living things take place

in aqueous environments (either inside or outside the cells)

• Water is needed to dissolve and transport nutrients, gases, etc. around us (blood, tissue fluid, saliva, sweat, etc)

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What are the properties of water?• Liquid at room temperature• Liquid water does not change temperature

quickly• High heat of vaporization• Frozen water is less dense than liquid water• Molecules of water cling together, “cohesion”

and to other polar substances “adhesion”• A good solvent for other polar (+/-) molecules

2.2 Water and living things

Water is a Water is a covalently bonded covalently bonded molecule that is also molecule that is also POLARPOLAR

(has +, - regions)(has +, - regions)• 2 Hydrogen atoms bond with an Oxygen atom at an

angle

• Region of the molecule where the O atom is located has a slightly neg.(-) charge, while the regions of the molecule where the two H+ atoms are have a slightly positive charge.

• Oxygen has a greater “custody” of the shared electrons

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Hydrogen BondsHydrogen Bonds • Hydrogen Bonds: negative part of the water molecule

(O) forms a bind with the positive charge of the H atoms – Relatively weak, singly, but rather strong collectively – Cause H2O molecules to cling together & to other

substances!

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Water’s polarity is responsible for some of its unique properties:

CohesionCohesion- • Water molecules are attracted

(+/-) to other nearby water molecules; bonds them together

• Surface tension = cohesive forces between water molecules are strong enough to act as if their was a "skin" in the water surface

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Water Properties

AdhesionAdhesion- • Water is attracted (+/-) to other substances.• meniscus = adhesive forces between water

molecules and glass

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Water PropertiesWater Properties

• Water is very important in temperature regulation - resists quick temperature changes and maintains homeostasis!

• H2O has a very high specific heat- which means it can absorb or lose a large amount of heat energy before its temperature changes.

• Thus, water has a moderating effect on temperatures (ex: body temp).

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Water PropertiesWater Properties• Water is less dense as a solid• As liquid water cools, it’s molecules slow

down and come closer together, until they reach 4°C.

• Below 4°C (approaching 0°C) they stop moving, and hydrogen bonds become fixed, rigid, and push apart, opening up spaces between the molecules– This is why ice floats, frozen bottles and

pipes burst22

Water is a almost-universal solventWater is a almost-universal solvent• Water is extremely important to all living

things, so the chemistry of living things often involves the study of solutions

• The polar (+/-) nature of water makes it a great solvent for other polar compounds to dissolve in.

• Hydrophilic or hydrophobic?

• What types of substances mix well with water?

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Know your terms• Solution: mixture in which

substances are uniformly distributed in another substance– Solutions can be mixtures of

liquids, solids, or gases• Solute: • Solvent:• Concentration [ ]:

measurement of the amount of solute dissolved in a fixed amount of solvent

• Saturated? • Aqueous solutions:

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Acids and bases• AcidsAcids are substances that dissociate and release hydrogen ions

(H+)• Ex: HCl H+ + Cl-

• BasesBases are substances that take up hydrogen atoms or release hydroxide ions (OH-)Ex: NaOH Na+ + OH-

Dissociation: molecules come apart when enough “pull” is exerted

• Pure water dissociates into H+ and OH- equally (hydrogen and hydroxide)

2.2 Water and living things

H2O H+ + OH-

Acids and Bases – the pH scaleAcids and Bases – the pH scale• Acidity and Alkalinity is a measure of the relative amount of

OH- and H+ ions in a solution!• pH= measure of how many H+ ions are in a solution

• Pure water has equal OH- and H+ ions in solution; pH of 7.0

• Acidic solutions have H+ > OH- ions– pH is below 7.0– Sour

• Basic solutions have H+ < OH- ions– pH is above 7.0– slippery and bitter

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Working scale is between 0 and 14 with 7 being neutralA pH below 7 is acidic and above 7 is basic

The concentration of ions between each whole number is a factor of 10

BuffersBuffers• …are chemical substances that neutralize small

amounts of either an acid or a base added to a solution

• Most chemical rxn’s in living organisms are controlled by pH, therefore...

• Buffers are very important for homeostasis.– If blood pH drops below 7.0 (acidosis), it could be fatal– If blood pH goes above 7.7 (alkalosis), it could be fatal

• If our blood did not contain a buffering system, we would not be able to drink and eat acidic/basic foods!

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Bicarbonate

Organic CompoundsOrganic Compounds• All compounds discovered can be classified

into two broad categories: inorganic and organic

• "Organic" = • The compounds of life consist of primarily 6

elements: "CHONPS"

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Chemistry of CARBON is the chemistry of LIFE!

• Carbon forms the “backbone” (framework) of all organic molecules

• C has four e- in its outermost energy level, but needs 8 to fill it, so it readily forms covalent bonds!

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Carbon, the basis for life

• Carbon likes to bond, with other atoms and with itself

• single bonds-

• double bonds-

• triple bonds-

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Simple & Complex MoleculesSimple & Complex Molecules• Molecules are often built up from smaller, simpler molecules:

MONOMERS

• Monomers bond together to produce: POLYMERS • Large polymers are called: MACROMOLECULES

• Dehydration reaction – the removal of water that allows subunits to link together into larger molecules

• Hydrolysis reaction – the addition of water that breaks larger molecules into their subunits

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There are Four Major Classes of Organic Compounds:

CARBOHYDRATES (= ENERGY)CARBOHYDRATES (= ENERGY)• - The most abundant organic compounds in nature

- C:H:O = approx. 1:2:1 MonosaccharidesMonosaccharides - simple sugars; "building blocks of all

carbs"• C6H12O6

Three main monosaccharides:• glucose- main source of energy for cells• fructose- sugar in fruits and honey (the sweetest

monosaccharide) • galactose- sugar in milk and yogurt 33

Carbohydrates, cont’d

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Disaccharides - two monosaccharides bonded together by dehydration rxn’s (form glycosidic bonds)

Examples:• glucose + fructose = sucrose (common table sugar)

•glucose + galactose = lactose (major sugar in milk)

What are “complex” carbohydrates?• Polysaccharides are made of

many carbon rings• Cell stores energy it doesn’t

need by converting monosaccharides into disaccharides/polysaccharides

• Starch is the storage form in plants

• • Glycogen- is the storage form

in animals – stored in liver and muscles- once

storage is full, glycogen turns to fat!

2.4 Carbohydrates

The Role of Enzymes in Starch Digestion(Amylase)

• Monosaccharides- soluble in water & CAN pass through cell membrane by diffusion

• Disaccharides- are soluble in water and CANNOT pass through the cell membrane (too BIG!)– when a cell needs energy, disaccharides are broken down into its monomers

by hydrolysis!

• Polysaccharides- are NOT soluble in water and CANNOT pass through the cell membrane without a series of hydrolysis rxn’s!

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What are lipids?What are lipids?

• Molecules that do not dissolve in water• Used as energy storage molecules, insulation,

cushion• Found in cell membranes • Found as fats and oils, waxes, phospholipids

and steroids

2.5 Lipids

How are fats and oils different?How are fats and oils different?

• FatsFats– Usually animal origin– Solid at room temperature– Function as long-term energy storage, insulation from heat

loss and cushion for organs

• OilsOils• Usually plant origin• Liquid at room temperature

2.5 Lipids

What is the structure of fats and oils?What is the structure of fats and oils?

• TRIGLYCERIDES: A glycerol molecule and 3 fatty acid tails

2.5 Lipids

Understanding fats when reading a Understanding fats when reading a nutrition labelnutrition label

• Recommendation for total amount of fat for a 2,000 calorie diet is 65g

• Be sure to know how many servings there are

• A % DV of 5% or less is low and 20% or more is high

• Try to stay away from trans fats

• Would you eat the food on the right? Why or why not?

2.5 Lipids

Trace elements: Are required by an organism in only minute quantities

Make up the remaining 4% of living matter

Table 2.1

(a) Nitrogen deficiency (b) Iodine deficiency

• The effects of essential element deficiencies

Figure 2.3

What is the structure of a What is the structure of a phospholipid?phospholipid?

• The structure is similar to a triglyceride.

• One fatty acid is replaced by a polar phosphate group.

• Phospholipids are the primary components of cellular membranes.

2.5 Lipids

Figure 2.19 Structure of a phospholipid.

Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.

inside cell

outside cell

b. Membrane structurea. Phospholipid structure

nonpolartails

polarhead

What are steroids?What are steroids?

• A lipid

• Structure is four fused carbon rings

Important steroids: Cholesterol, testosterone,

estrogen, progesterone, cortisol

2.5 Lipids

What are proteins?What are proteins?• Large and often complicated molecules• Make up skin, muscles, pigments, antibodies,

hormones & enzymes• Hundreds of thousands of different kinds in

each cell• Mostly C,H,O, & N • Composed of amino acid monomers (20 AA

groups in total)• Can denature, change in shape, that causes

loss of function

2.6 Proteins

What do amino acids look like?What do amino acids look like?2.6 Proteins

What do the levels of organization What do the levels of organization look like?look like?

2.6 Proteins

• Support: keratin (hairs, nails) , collagen (ligaments, tendons, skin)

• Transport: channel proteins allow certain molecules through cell membranes; hemoglobin transports oxygen (RBC)

• Defense: antibodies are protein made by WBC

• Hormones: regulate cell metabolism and growth (ex: insulin)

• Motion: muscle tissue made of contractile proteins (actin & myosin)

• Enzymes: catalyze chemical reactions in cells48

ENZYMESENZYMES are important proteins• Many chemical reactions in living cells (and organisms) are

regulated by ENZYMES• Enzymes are globular proteins in living systems that mediate

metabolic reactions (make and break chemical bonds)

– Metabolism: the series of energy exchanges and chemical reactions that occur in living systems (cells, organisms)

– catabolic activities = breakdown of larger molecules into smaller; AB ==> A + B

– anabolic activities = synthesis of larger molecules from smaller ones; A + B ==> AB

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What are nucleic acids?What are nucleic acids?

• Made of nucleotide subunits

• Function in the cell to make proteins

• Directs traits and behaviors

• Includes RNA and DNA

2.7 Nucleic acids

NUCLEIC ACIDSNUCLEIC ACIDS • Nucleic acids are long chains (polymers)of

nucleotides• Nucleotides are the monomers of nucleic acids

Each nucleotide includes a nitrogenous base, 5-C sugar, and phosphate group

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DNA: Deoxyribonucleic acidDNA: Deoxyribonucleic acid• Contains genetic

information• Composed of:

1) Deoxyribose sugar2) Phosphate group3) 4 different “base" groups:

Adenine, Guanine, Cytosine, and Thymine

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RNA: Ribonucleic acidRNA: Ribonucleic acid• Stores and transfers genetic information for

making proteins from nucleus to ribosomes• Like DNA, RNA is composed of nucleotides:

1) Ribose sugar2) Phosphate group3) 4 different “base" groups: Adenine, Guanine,

Cytosine, and Uracil

• DNA IS DOUBLE STRANDED AND RNA IS SINGLE STRANDED!

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Summary of the macromoleculesSummary of the macromolecules